Chlorine in PDB 7bek: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2), PDB code: 7bek was solved by D.Zhou, Y.Zhao, J.Ren, D.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.71 / 2.04
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	83.02, 149.41, 145.49, 90, 90, 90
R / Rfree (%)	20 / 22

The binding sites of Chlorine atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) (pdb code 7bek). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2), PDB code: 7bek:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl504 b:76.3 occ:1.00 N H:VAL156 3.2 42.3 1.0 O H:HOH749 3.2 66.8 1.0 O H:HOH632 3.5 57.0 1.0 CA H:THR155 3.5 47.9 1.0 O H:VAL156 3.6 43.0 1.0 C H:THR155 3.9 52.3 1.0 CB H:THR155 4.0 47.6 1.0 CA H:VAL156 4.2 43.1 1.0 O H:VAL154 4.3 48.0 1.0 C H:VAL156 4.3 46.4 1.0 CG2 H:THR155 4.4 44.2 1.0 CG2 H:THR169 4.4 47.5 1.0 CB H:VAL156 4.5 48.9 1.0 N H:THR155 4.7 46.9 1.0 CB H:THR169 4.8 46.0 1.0 OG1 H:THR169 4.8 45.2 1.0 C H:VAL154 4.9 48.1 1.0 CG2 H:VAL156 4.9 37.5 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl505 b:88.9 occ:1.00 N H:ASN73 3.3 64.4 1.0 CG H:ASN73 3.8 77.4 1.0 OD1 H:ASN73 3.8 72.7 1.0 CB H:ASN73 3.9 72.1 1.0 CA H:ASP72 4.0 63.1 1.0 O H:ARG71 4.0 59.9 1.0 C H:ASP72 4.1 67.8 1.0 CA H:ASN73 4.2 67.5 1.0 CL H:CL506 4.2 91.8 1.0 ND2 H:ASN73 4.3 80.9 1.0 OD1 H:ASP72 4.3 80.2 1.0 C H:ARG71 4.8 56.1 1.0 CG H:ASP72 4.8 72.6 1.0 N H:ASP72 4.8 60.4 1.0 CB H:ASP72 5.0 69.5 1.0 N H:SER74 5.0 72.5 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl506 b:91.8 occ:1.00 ND2 H:ASN73 2.9 80.9 1.0 OD1 H:ASN73 3.0 72.7 1.0 CG H:ASN73 3.3 77.4 1.0 NE H:ARG71 3.5 54.8 1.0 NH2 H:ARG71 3.6 54.3 1.0 CZ H:ARG71 4.1 59.0 1.0 CL H:CL505 4.2 88.9 1.0 CB H:SER30 4.5 52.8 1.0 CG H:ARG71 4.6 58.8 1.0 CD H:ARG71 4.6 55.8 1.0 CB H:ASN73 4.7 72.1 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl504 b:80.8 occ:1.00 O L:HOH601 2.4 67.7 1.0 O L:HOH627 2.7 61.2 1.0 N L:GLY212 3.2 62.4 1.0 CA L:ARG211 3.9 58.4 1.0 O L:ASN210 4.0 53.5 1.0 CA L:GLY212 4.0 65.5 1.0 C L:ARG211 4.1 59.5 1.0 OH L:TYR186 4.1 50.3 1.0 O L:GLU213 4.2 83.4 1.0 CB L:PRO119 4.3 34.2 1.0 CD2 L:PHE209 4.4 46.6 1.0 C L:GLY212 4.4 78.5 1.0 CE2 L:PHE209 4.5 41.4 1.0 N L:GLU213 4.5 74.7 1.0 CG L:PRO119 4.7 51.4 1.0 C L:ASN210 4.8 50.5 1.0 N L:ARG211 4.8 51.3 1.0 CG L:ARG211 4.8 53.8 1.0 CB L:ARG211 4.9 53.0 1.0 O L:HOH676 4.9 62.8 1.0 C L:GLU213 4.9 78.2 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl505 b:81.2 occ:1.00 N L:GLU143 3.1 52.4 1.0 CB L:GLU143 3.3 58.6 1.0 CG L:ARG142 3.6 65.4 1.0 CB L:PRO141 3.6 49.2 1.0 N L:ARG142 3.7 52.3 1.0 CA L:GLU143 3.8 55.9 1.0 CG L:PRO141 4.0 51.4 1.0 O L:HOH649 4.1 53.3 1.0 C L:ARG142 4.1 53.0 1.0 CA L:ARG142 4.3 55.4 1.0 OE1 L:GLU143 4.3 96.6 1.0 C L:PRO141 4.3 49.2 1.0 CB L:ARG142 4.5 61.4 1.0 CA L:PRO141 4.6 50.2 1.0 CG L:GLU143 4.6 69.0 1.0 CD L:ARG142 4.7 63.9 1.0 O L:HOH660 4.8 63.8 1.0 CD L:GLU143 4.9 88.5 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-158 Fab (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl704 b:81.9 occ:1.00 NZ E:LYS424 3.0 50.2 1.0 CA E:GLY413 3.8 54.7 1.0 C E:GLY413 3.8 54.2 1.0 O E:GLN414 3.8 48.5 1.0 O E:HOH812 4.0 46.4 1.0 CE E:LYS424 4.0 43.7 1.0 O E:GLY413 4.1 50.9 1.0 N E:GLN414 4.2 43.3 1.0 O E:HOH813 4.3 48.2 1.0 N E:GLY413 4.5 49.2 1.0 CG2 E:THR415 4.5 46.5 1.0 C E:GLN414 4.6 49.3 1.0 OD1 E:ASP427 4.6 64.5 1.0

W.Dejnirattisai, D.Zhou, H.M.Ginn, H.M.Duyvesteyn, P.Supasa, J.B.Case, Y.Zhao, T.S.Walter, A.J.Mentzer, C.Liu, B.Wang, G.C.Paesen, J.Slon-Campos, C.Lopez-Camacho, N.M.Kafai, A.L.Bailey, R.E.Chen, B.Ying, C.Thompson, J.Bolton, A.Fyfe, S.Gupta, T.K.Tan, J.Gilbert-Jaramillo, W.James, M.Knight, M.W.Carroll, D.Skelly, C.Dold, Y.Peng, R.Levin, T.Dong, A.J.Pollard, J.C.Knight, P.Klenerman, N.Temperton, D.R.Hall, M.A.Williams, N.G.Paterson, F.K.Bertram, C.A.Seibert, D.K.Clare, A.Howe, J.Raedecke, Y.Song, A.R.Townsend, K.Y.A.Huang, E.E.Fry, J.Mongkolsapaya, M.S.Diamond, J.Ren, D.I.Stuart, G.R.Screaton. The Antigenic Anatomy of Sars-Cov-2 Receptor Binding Domain Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.02.032